Baking only light maps in Cycles
We are doing the exact same thing, although my approach to the problem is slightly different.
Like you I created a second UV channel for the lightmap while handling the other materials on the first one. Once I unwrapped the object to the second UV channel I duplicate the entire object, remove all the materials from the clone and add a simple white material to it.
Then things start to get a bit complicated. Let's say there are several objects, for example a wall, a floor and a ceiling. When I bake the wall, I activate the clone of the wall, while hiding the original wall object. The original floor and ceiling objects stay active while their clones are hidden. This way you can retain the bounce light data that comes from the unchanged original objects.
It is basically the same procedure as having a second node tree in the materials except that you're switching on and off objects instead of node trees in every material on the scene.
I'm not sure if this is the smartest way to do it, but I don't have to bake several passes this way...